MolNFT v1 · #4921 · protein

HPT + HMTT

1E2M · Thymidine kinase: “HPT + HMTT”. X-ray diffraction, 2 ligands (HPT, SO4), 9 pockets (best druggability 0.78). MolNFT v1 #4921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1E2M
Type: protein
Length: 615 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidine kinase
EC: 2.7.1.21
UniProt: P03176
Ligands: HPT, SO4
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidine kinase (EC 2.7.1.21)	protein	305	57% helix, 13% strand	P03176
B	Thymidine kinase (EC 2.7.1.21)	protein	310	57% helix, 12% strand	P03176

Ligands and binding sites

HPT · 6-hydroxypropylthymine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.78	0.98	19	HPT
2	218	0.60	0.80	28	SO4, HPT
3	285	0.59	0.78	48	empty
4	88	0.44	0.80	20	empty
5	107	0.44	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 1702 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1E2M · HPT + HMTT · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P03176
Elsewhere: RCSB PDB 1E2M · PDBe 1E2M · UniProt P03176

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